[BioC] CDF package in R (windows)
James W. MacDonald
jmacdon at med.umich.edu
Thu Jun 7 15:23:40 CEST 2007
Salim Charaniya wrote:
> Thanks a lot...
> I was able to execute the command R CMD INSTALL cdfpackage. unfortunately there is an error during execution.
> the first few steps go well (adding build stamp to DESCRIPTION, installing R files, data files, man source files,....installing help)
> (i noticed that a subdirectory named 'chm' is created in packagecdf during execution)
> The execution malfunctions at this point and i get the following error
> hhc: not found
You should re-check your path. This indicates that you _don't_ have the
MS HTML workshop in your path.
You could also do rcmd install --docs=txt,html,latex <packagename> which
won't build the chm help.
> cp: cannot stat 'c://packagecdf/chm/packagecdf.chm' no such file or directory
> make: ***[chm-packagecdf] Error 1
> *** Installation of packagecdf failed ***
> Acc to the manual .chm file is created by microsoft help html workshop which i have installed on the computer (and also added to the path). Any idea why i am still getting this error?
> Sorry for bothering you guys
> Thanks again
> ----- Original Message ----
> From: Seth Falcon <sfalcon at fhcrc.org>
> To: Salim Charaniya <sal_charaniya at yahoo.com>
> Cc: bioconductor at stat.math.ethz.ch
> Sent: Wednesday, June 6, 2007 4:35:40 PM
> Subject: Re: [BioC] CDF package in R (windows)
> Salim Charaniya <sal_charaniya at yahoo.com> writes:
>>Hi all, i am a relatively new user of bioconductor. i am using R 2.5.0
>>installed on windows. I have used bioconductor for processing affy
>>data. Last few days i have been trying to develop a CDF package for a
>>custom affy array. I downloaded the makecdfenv package and used the
>>commands in there to create a cdf package (using the .cdf file). but
>>it seems that is not enough in windows environment. I have read the
>>instructions in R installation and admin manual. Accordingly i
>>installed the windows toolset (active perl, command line tools and
>>MinGW compilers (Rtools.exe), inno setup installer). I have also
>>changed the path according to the instructions in Rtools.txt. However,
>>I cannot understand the following statement in the R manual:
>>There are a number of options available: use R CMD INSTALL
>>The same command works in Windows if you have the source-code package
>>files (option “Source Package Installation Files” in the installer)
>>and toolset (see The Windows toolset) installed.
>>I have tried this command (R cmd install path_for_cdfpackage). But it
>>is not recognized as a command and i get an error. What are these
>>source-code package files? Where can i get them? Is there anything
>>else that i need to do to create the cdf package?
> Is the bin directory of your R also in your PATH? Your efforts with
> makecdfenv should have produced a source package directory. Can you
> c:\<your_path_here>\R-2.5.0\bin\R CMD INSTALL somecdfpackagedir
> I think you are close to getting things to work.
> + seth
James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
More information about the Bioconductor